Mercurial > repos > iuc > sra_tools
comparison sam_dump.xml @ 10:8c00bc7fd8de draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 48c9d7f30655d48c9b46b9ca7a17c454eb54694d
author | iuc |
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date | Fri, 17 Nov 2017 13:22:37 -0500 |
parents | 6c60903f70ac |
children | c38286ea7047 |
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9:6c60903f70ac | 10:8c00bc7fd8de |
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1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.2"> | 1 <tool id="sam_dump" name="Download and Extract Reads in BAM" version="@VERSION@.3"> |
2 <description>format from NCBI SRA</description> | 2 <description>format from NCBI SRA</description> |
3 <macros> | 3 <macros> |
4 <import>sra_macros.xml</import> | 4 <import>sra_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <version_command>sam-dump --version</version_command> | 7 <version_command>sam-dump --version</version_command> |
8 <command detect_errors="exit_code"> | 8 <command detect_errors="exit_code"> |
9 <![CDATA[ | 9 <![CDATA[ |
10 #if $input.input_select=="file_list": | 10 #if $input.input_select=="file_list": |
11 for acc in `cat $input.file_list` ; | 11 for acc in `cat $input.file_list` ; |
12 do | 12 do |
13 #elif $input.input_select=="accession_number": | 13 #elif $input.input_select=="accession_number": |
14 acc="${input.accession}" && | 14 acc="${input.accession}" && |
15 #end if | 15 #end if |
16 | 16 |
17 #if $input.input_select=="file_list" or $input.input_select=="accession_number": | 17 #if $input.input_select=="file_list" or $input.input_select=="accession_number": |
18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( | 18 [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && ( |
19 #end if | 19 #end if |
20 | |
21 | |
22 | 20 |
23 ## Need to set the home directory to the current working directory, | 21 ## Need to set the home directory to the current working directory, |
24 ## else the tool tries to write to home/.ncbi and fails when used | 22 ## else the tool tries to write to home/.ncbi and fails when used |
25 ## with a cluster manager. | 23 ## with a cluster manager. |
26 export HOME=\$PWD && | 24 export HOME=\$PWD && |
36 ## dump command. | 34 ## dump command. |
37 vdb-config -s "/repository/user/main/public/root=\$PWD" && | 35 vdb-config -s "/repository/user/main/public/root=\$PWD" && |
38 #end if | 36 #end if |
39 sam-dump --log-level fatal --disable-multithreading | 37 sam-dump --log-level fatal --disable-multithreading |
40 #if str( $adv.region ) != "": | 38 #if str( $adv.region ) != "": |
41 --aligned-region "$adv.region" | 39 --aligned-region '$adv.region' |
42 #end if | 40 #end if |
43 #if str( $adv.matepairDist ) != "": | 41 #if str( $adv.matepairDist ) != "": |
44 --matepair-distance "$adv.matepairDist" | 42 --matepair-distance '$adv.matepairDist' |
45 #end if | 43 #end if |
46 #if str( $adv.minMapq ) != "": | 44 #if str( $adv.minMapq ) != "": |
47 --min-mapq "$adv.minMapq" | 45 --min-mapq '$adv.minMapq' |
48 #end if | 46 #end if |
49 #if str( $adv.header ) == "yes": | 47 --header |
50 --header | |
51 #else: | |
52 --no-header | |
53 #end if | |
54 #if str( $adv.alignments ) == "both": | 48 #if str( $adv.alignments ) == "both": |
55 --unaligned | 49 --unaligned |
56 #end if | 50 #end if |
57 #if str( $adv.alignments ) == "unaligned": | 51 #if str( $adv.alignments ) == "unaligned": |
58 --unaligned-spots-only | 52 --unaligned-spots-only |
59 #end if | 53 #end if |
60 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): | 54 #if (str( $adv.primary ) == "yes") and (str ( $adv.alignments != "unaligned") ): |
61 --primary | 55 --primary |
62 #end if | 56 #end if |
63 #if $input.input_select == "file": | 57 #if $input.input_select == "file": |
64 "$input.file" | 58 '$input.file' |
65 #elif $input.input_select == "accession_number": | 59 #elif $input.input_select == "accession_number": |
66 "\$acc" | 60 "\$acc" |
67 #elif $input.input_select=="file_list": | 61 #elif $input.input_select=="file_list": |
68 "\$acc" | 62 "\$acc" |
69 #end if | 63 #end if |
70 | 64 |
71 #if str( $outputformat ) == "bam": | 65 #if str( $outputformat ) == "bam": |
72 | samtools view -Sb - 2> /dev/null | 66 | samtools view -Sb - 2> /dev/null |
73 #end if | 67 #end if |
74 #if $input.input_select == "file": | 68 #if $input.input_select == "file": |
75 > "$output_file" | 69 > '$output_file' |
76 #elif $input.input_select == "accession_number": | 70 #elif $input.input_select == "accession_number": |
77 > "$output_accession" ) | 71 > '$output_accession' ) |
78 #end if | 72 #end if |
79 | 73 |
80 #if $input.input_select=="file_list": | 74 #if $input.input_select=="file_list": |
81 #if str( $outputformat ) == "bam": | 75 #if str( $outputformat ) == "bam": |
82 > "\$acc.bam" | 76 > "\$acc.bam" |
84 > "\$acc.sam" | 78 > "\$acc.sam" |
85 #end if | 79 #end if |
86 ) ; done | 80 ) ; done |
87 #end if | 81 #end if |
88 | 82 |
89 | |
90 ]]> | 83 ]]> |
91 </command> | 84 </command> |
92 <inputs> | 85 <inputs> |
93 <expand macro="input_conditional"/> | 86 <expand macro="input_conditional"/> |
94 <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools."> | 87 <param name="outputformat" type="select" display="radio" label="select output format" help="In vast majority of cases you want to download data in bam format. It is more compact and is accepted by all downstream tools."> |
95 <option value="bam">bam</option> | 88 <option value="bam">bam</option> |
96 <option value="sam">sam</option> | 89 <option value="sam">sam</option> |
97 </param> | 90 </param> |
98 <section name="adv" title="Advanced Options" expanded="False"> | 91 <section name="adv" title="Advanced Options" expanded="False"> |
99 <param name="header" type="select" value="yes"> | |
100 <label>output header</label> | |
101 <option value="yes">Yes</option> | |
102 <option value="no">No</option> | |
103 </param> | |
104 <expand macro="alignments"/> | 92 <expand macro="alignments"/> |
105 <expand macro="region"/> | 93 <expand macro="region"/> |
106 <expand macro="matepairDist"/> | 94 <expand macro="matepairDist"/> |
107 <param name="primary" type="select" value="no"> | 95 <param name="primary" type="select" value="no"> |
108 <label>only primary aligments</label> | 96 <label>only primary aligments</label> |
139 <param name="region" value="17:41243452-41277500"/> | 127 <param name="region" value="17:41243452-41277500"/> |
140 <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/> | 128 <output name="output_accession" file="sam_dump_result.sam" compare="contains" ftype="sam"/> |
141 </test> | 129 </test> |
142 </tests> | 130 </tests> |
143 <help><![CDATA[ | 131 <help><![CDATA[ |
132 | |
144 **What it does?** | 133 **What it does?** |
145 | 134 |
146 This tool extracts data (in BAM_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump_ utility of the SRA Toolkit. | 135 This tool extracts data (in BAM_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the sam-dump_ utility of the SRA Toolkit. |
147 | 136 |
148 **How to use it?** | 137 **How to use it?** |
189 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf | 178 .. _BAM: https://samtools.github.io/hts-specs/SAMv1.pdf |
190 .. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html | 179 .. _sam-dump: http://ncbi.github.io/sra-tools/sam-dump.html |
191 .. _collection: https://galaxyproject.org/tutorials/collections/ | 180 .. _collection: https://galaxyproject.org/tutorials/collections/ |
192 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies | 181 .. _link: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies |
193 | 182 |
194 | |
195 @SRATOOLS_ATTRRIBUTION@ | 183 @SRATOOLS_ATTRRIBUTION@ |
196 ]]></help> | 184 ]]></help> |
197 <expand macro="citation"/> | 185 <expand macro="citation"/> |
198 </tool> | 186 </tool> |